Multiple sequence alignment - TraesCS1D01G388000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G388000 chr1D 100.000 4562 0 0 1 4562 460189935 460194496 0.000000e+00 8425
1 TraesCS1D01G388000 chr1D 94.790 499 19 4 2409 2905 90272087 90272580 0.000000e+00 771
2 TraesCS1D01G388000 chr1D 82.927 205 25 6 4294 4494 459523740 459523542 4.690000e-40 176
3 TraesCS1D01G388000 chr1D 82.927 205 25 6 4294 4494 459624323 459624521 4.690000e-40 176
4 TraesCS1D01G388000 chr1A 92.467 2323 113 29 2257 4559 551745190 551747470 0.000000e+00 3264
5 TraesCS1D01G388000 chr1A 87.677 917 58 23 937 1811 551744286 551745189 0.000000e+00 1016
6 TraesCS1D01G388000 chr1A 93.694 555 24 7 2362 2910 253946167 253946716 0.000000e+00 821
7 TraesCS1D01G388000 chr1A 88.186 474 24 20 1 447 551743592 551744060 1.870000e-148 536
8 TraesCS1D01G388000 chr1A 92.000 200 5 1 659 858 551744057 551744245 2.090000e-68 270
9 TraesCS1D01G388000 chr1A 84.559 272 31 6 4294 4562 551533993 551533730 4.530000e-65 259
10 TraesCS1D01G388000 chr1B 93.233 1788 81 20 2800 4562 632718919 632720691 0.000000e+00 2595
11 TraesCS1D01G388000 chr1B 90.561 784 62 7 1865 2636 632718119 632718902 0.000000e+00 1027
12 TraesCS1D01G388000 chr1B 84.917 968 70 26 949 1870 632715680 632716617 0.000000e+00 909
13 TraesCS1D01G388000 chr3A 92.577 714 35 12 2204 2910 439566105 439565403 0.000000e+00 1009
14 TraesCS1D01G388000 chr3A 82.000 450 50 17 1397 1824 439566551 439566111 2.020000e-93 353
15 TraesCS1D01G388000 chr6A 93.514 555 24 8 2362 2910 493359952 493359404 0.000000e+00 815
16 TraesCS1D01G388000 chr2A 95.400 500 15 5 2409 2905 758443760 758444254 0.000000e+00 789
17 TraesCS1D01G388000 chr2A 94.800 500 17 6 2409 2905 691517223 691516730 0.000000e+00 771
18 TraesCS1D01G388000 chr7D 95.171 497 17 4 2411 2905 105980780 105981271 0.000000e+00 778
19 TraesCS1D01G388000 chr5A 94.589 499 20 4 2409 2905 267322730 267323223 0.000000e+00 765
20 TraesCS1D01G388000 chr3B 90.909 110 10 0 985 1094 479296738 479296847 1.020000e-31 148
21 TraesCS1D01G388000 chr3D 92.222 90 7 0 987 1076 367307014 367307103 1.330000e-25 128


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G388000 chr1D 460189935 460194496 4561 False 8425.000000 8425 100.000000 1 4562 1 chr1D.!!$F3 4561
1 TraesCS1D01G388000 chr1A 551743592 551747470 3878 False 1271.500000 3264 90.082500 1 4559 4 chr1A.!!$F2 4558
2 TraesCS1D01G388000 chr1A 253946167 253946716 549 False 821.000000 821 93.694000 2362 2910 1 chr1A.!!$F1 548
3 TraesCS1D01G388000 chr1B 632715680 632720691 5011 False 1510.333333 2595 89.570333 949 4562 3 chr1B.!!$F1 3613
4 TraesCS1D01G388000 chr3A 439565403 439566551 1148 True 681.000000 1009 87.288500 1397 2910 2 chr3A.!!$R1 1513
5 TraesCS1D01G388000 chr6A 493359404 493359952 548 True 815.000000 815 93.514000 2362 2910 1 chr6A.!!$R1 548

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
587 615 0.171903 CCGCATTGCTGGAGGAAAAG 59.828 55.0 12.34 0.0 0.00 2.27 F
1355 1416 0.179150 CTCGCCGAGTTCTTCCTCTG 60.179 60.0 5.82 0.0 0.00 3.35 F
2111 3733 0.107993 TTGCGAAGAGGAGGAGCATG 60.108 55.0 0.00 0.0 37.68 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 3667 0.110056 GTTCACTGTCGCTGCAATGG 60.110 55.0 0.00 0.0 0.00 3.16 R
3303 4937 0.100682 GCTGCTCCTCGTCGTAATCA 59.899 55.0 0.00 0.0 0.00 2.57 R
3979 5632 0.796312 AGTAAGCAATTCACGGTGCG 59.204 50.0 2.51 0.0 45.62 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 5.059404 ACATTTCCCGAAATCATGAACAC 57.941 39.130 0.00 0.00 38.84 3.32
97 101 9.875675 TTTTGAAAACATGAACAAGTTTTTCAG 57.124 25.926 17.49 5.49 45.09 3.02
199 204 6.801377 TGTGAACAATATTGAAAAGATGCGAC 59.199 34.615 22.16 4.56 0.00 5.19
200 205 6.801377 GTGAACAATATTGAAAAGATGCGACA 59.199 34.615 22.16 3.03 0.00 4.35
212 219 7.226325 TGAAAAGATGCGACATTTTTGGAATTT 59.774 29.630 8.38 0.00 0.00 1.82
216 223 8.600449 AGATGCGACATTTTTGGAATTTTAAA 57.400 26.923 0.00 0.00 0.00 1.52
348 376 7.352739 TCGAACAATTTCTTAAGTTTCTGAGC 58.647 34.615 1.63 0.00 0.00 4.26
350 378 7.322222 CGAACAATTTCTTAAGTTTCTGAGCAG 59.678 37.037 1.63 0.00 0.00 4.24
359 387 4.142609 AGTTTCTGAGCAGTTGTTGAGA 57.857 40.909 0.00 0.00 0.00 3.27
383 411 9.408648 AGAAATGAAAGAAAACTAAGAACAGGA 57.591 29.630 0.00 0.00 0.00 3.86
433 461 6.951062 AAAGAGAGAAAAGAAACAGGGAAG 57.049 37.500 0.00 0.00 0.00 3.46
437 465 6.100424 AGAGAGAAAAGAAACAGGGAAGAAGA 59.900 38.462 0.00 0.00 0.00 2.87
440 468 7.615757 AGAGAAAAGAAACAGGGAAGAAGAAAA 59.384 33.333 0.00 0.00 0.00 2.29
443 471 5.500645 AGAAACAGGGAAGAAGAAAAACG 57.499 39.130 0.00 0.00 0.00 3.60
447 475 5.907866 ACAGGGAAGAAGAAAAACGAAAA 57.092 34.783 0.00 0.00 0.00 2.29
448 476 6.275494 ACAGGGAAGAAGAAAAACGAAAAA 57.725 33.333 0.00 0.00 0.00 1.94
449 477 6.330278 ACAGGGAAGAAGAAAAACGAAAAAG 58.670 36.000 0.00 0.00 0.00 2.27
450 478 6.152154 ACAGGGAAGAAGAAAAACGAAAAAGA 59.848 34.615 0.00 0.00 0.00 2.52
451 479 7.033185 CAGGGAAGAAGAAAAACGAAAAAGAA 58.967 34.615 0.00 0.00 0.00 2.52
452 480 7.544217 CAGGGAAGAAGAAAAACGAAAAAGAAA 59.456 33.333 0.00 0.00 0.00 2.52
453 481 7.544566 AGGGAAGAAGAAAAACGAAAAAGAAAC 59.455 33.333 0.00 0.00 0.00 2.78
454 482 7.329962 GGGAAGAAGAAAAACGAAAAAGAAACA 59.670 33.333 0.00 0.00 0.00 2.83
455 483 8.160342 GGAAGAAGAAAAACGAAAAAGAAACAC 58.840 33.333 0.00 0.00 0.00 3.32
456 484 8.812147 AAGAAGAAAAACGAAAAAGAAACACT 57.188 26.923 0.00 0.00 0.00 3.55
457 485 9.902196 AAGAAGAAAAACGAAAAAGAAACACTA 57.098 25.926 0.00 0.00 0.00 2.74
458 486 9.902196 AGAAGAAAAACGAAAAAGAAACACTAA 57.098 25.926 0.00 0.00 0.00 2.24
491 519 2.129620 AAAAACCCGGCTGGAAACC 58.870 52.632 15.09 0.00 37.49 3.27
492 520 0.397957 AAAAACCCGGCTGGAAACCT 60.398 50.000 15.09 0.00 37.49 3.50
493 521 0.826256 AAAACCCGGCTGGAAACCTC 60.826 55.000 15.09 0.00 37.49 3.85
494 522 2.708593 AAACCCGGCTGGAAACCTCC 62.709 60.000 15.09 0.00 42.81 4.30
495 523 4.778143 CCCGGCTGGAAACCTCCG 62.778 72.222 15.09 12.33 45.85 4.63
496 524 3.702048 CCGGCTGGAAACCTCCGA 61.702 66.667 5.28 0.00 45.85 4.55
497 525 2.345991 CGGCTGGAAACCTCCGAA 59.654 61.111 13.44 0.00 45.85 4.30
498 526 1.741770 CGGCTGGAAACCTCCGAAG 60.742 63.158 13.44 0.00 45.85 3.79
511 539 4.716003 CGAAGGTTCCCAGAACCC 57.284 61.111 20.22 7.58 41.18 4.11
512 540 1.375523 CGAAGGTTCCCAGAACCCG 60.376 63.158 20.22 14.58 41.18 5.28
513 541 1.002502 GAAGGTTCCCAGAACCCGG 60.003 63.158 20.22 0.00 41.18 5.73
514 542 1.462627 AAGGTTCCCAGAACCCGGA 60.463 57.895 20.22 0.00 41.18 5.14
515 543 0.845102 AAGGTTCCCAGAACCCGGAT 60.845 55.000 20.22 2.03 41.18 4.18
516 544 1.223763 GGTTCCCAGAACCCGGATC 59.776 63.158 14.38 0.00 34.26 3.36
517 545 1.153429 GTTCCCAGAACCCGGATCG 60.153 63.158 0.73 0.00 0.00 3.69
518 546 3.026431 TTCCCAGAACCCGGATCGC 62.026 63.158 0.73 0.00 0.00 4.58
519 547 3.470888 CCCAGAACCCGGATCGCT 61.471 66.667 0.73 0.00 0.00 4.93
520 548 2.107141 CCAGAACCCGGATCGCTC 59.893 66.667 0.73 0.00 0.00 5.03
521 549 2.721167 CCAGAACCCGGATCGCTCA 61.721 63.158 0.73 0.00 0.00 4.26
522 550 1.218047 CAGAACCCGGATCGCTCAA 59.782 57.895 0.73 0.00 0.00 3.02
523 551 0.391130 CAGAACCCGGATCGCTCAAA 60.391 55.000 0.73 0.00 0.00 2.69
524 552 0.391263 AGAACCCGGATCGCTCAAAC 60.391 55.000 0.73 0.00 0.00 2.93
525 553 1.693083 GAACCCGGATCGCTCAAACG 61.693 60.000 0.73 0.00 0.00 3.60
526 554 3.564027 CCCGGATCGCTCAAACGC 61.564 66.667 0.73 0.00 0.00 4.84
527 555 2.509336 CCGGATCGCTCAAACGCT 60.509 61.111 0.00 0.00 0.00 5.07
528 556 2.517450 CCGGATCGCTCAAACGCTC 61.517 63.158 0.00 0.00 0.00 5.03
529 557 2.849966 CGGATCGCTCAAACGCTCG 61.850 63.158 0.00 0.00 0.00 5.03
530 558 2.318024 GATCGCTCAAACGCTCGC 59.682 61.111 0.00 0.00 0.00 5.03
531 559 2.125912 ATCGCTCAAACGCTCGCT 60.126 55.556 0.00 0.00 0.00 4.93
532 560 2.072038 GATCGCTCAAACGCTCGCTC 62.072 60.000 0.00 0.00 0.00 5.03
533 561 2.549611 ATCGCTCAAACGCTCGCTCT 62.550 55.000 0.00 0.00 0.00 4.09
534 562 2.375766 CGCTCAAACGCTCGCTCTT 61.376 57.895 0.00 0.00 0.00 2.85
535 563 1.417979 GCTCAAACGCTCGCTCTTC 59.582 57.895 0.00 0.00 0.00 2.87
536 564 1.011451 GCTCAAACGCTCGCTCTTCT 61.011 55.000 0.00 0.00 0.00 2.85
537 565 0.988439 CTCAAACGCTCGCTCTTCTC 59.012 55.000 0.00 0.00 0.00 2.87
538 566 0.598562 TCAAACGCTCGCTCTTCTCT 59.401 50.000 0.00 0.00 0.00 3.10
539 567 0.712775 CAAACGCTCGCTCTTCTCTG 59.287 55.000 0.00 0.00 0.00 3.35
540 568 1.011451 AAACGCTCGCTCTTCTCTGC 61.011 55.000 0.00 0.00 0.00 4.26
541 569 2.581953 CGCTCGCTCTTCTCTGCC 60.582 66.667 0.00 0.00 0.00 4.85
542 570 2.891882 GCTCGCTCTTCTCTGCCT 59.108 61.111 0.00 0.00 0.00 4.75
543 571 1.519013 GCTCGCTCTTCTCTGCCTG 60.519 63.158 0.00 0.00 0.00 4.85
544 572 1.889454 CTCGCTCTTCTCTGCCTGT 59.111 57.895 0.00 0.00 0.00 4.00
545 573 0.458197 CTCGCTCTTCTCTGCCTGTG 60.458 60.000 0.00 0.00 0.00 3.66
546 574 2.099431 CGCTCTTCTCTGCCTGTGC 61.099 63.158 0.00 0.00 38.26 4.57
547 575 2.099431 GCTCTTCTCTGCCTGTGCG 61.099 63.158 0.00 0.00 41.78 5.34
548 576 1.291588 CTCTTCTCTGCCTGTGCGT 59.708 57.895 0.00 0.00 41.78 5.24
549 577 1.005748 TCTTCTCTGCCTGTGCGTG 60.006 57.895 0.00 0.00 41.78 5.34
550 578 2.666190 TTCTCTGCCTGTGCGTGC 60.666 61.111 0.00 0.00 41.78 5.34
553 581 3.914605 CTCTGCCTGTGCGTGCGTA 62.915 63.158 0.00 0.00 41.78 4.42
554 582 3.481903 CTGCCTGTGCGTGCGTAG 61.482 66.667 0.00 0.00 41.78 3.51
555 583 3.914605 CTGCCTGTGCGTGCGTAGA 62.915 63.158 0.00 0.00 41.78 2.59
556 584 3.479269 GCCTGTGCGTGCGTAGAC 61.479 66.667 0.00 0.00 0.00 2.59
557 585 2.258591 CCTGTGCGTGCGTAGACT 59.741 61.111 0.00 0.00 0.00 3.24
558 586 1.801913 CCTGTGCGTGCGTAGACTC 60.802 63.158 0.00 0.00 0.00 3.36
559 587 2.127003 TGTGCGTGCGTAGACTCG 60.127 61.111 0.00 0.00 0.00 4.18
560 588 2.175078 GTGCGTGCGTAGACTCGA 59.825 61.111 0.00 0.00 0.00 4.04
561 589 2.144680 GTGCGTGCGTAGACTCGAC 61.145 63.158 0.00 0.00 0.00 4.20
562 590 2.175078 GCGTGCGTAGACTCGACA 59.825 61.111 0.00 0.00 0.00 4.35
563 591 1.441515 GCGTGCGTAGACTCGACAA 60.442 57.895 0.00 0.00 0.00 3.18
564 592 0.797249 GCGTGCGTAGACTCGACAAT 60.797 55.000 0.00 0.00 0.00 2.71
565 593 1.614385 CGTGCGTAGACTCGACAATT 58.386 50.000 0.00 0.00 0.00 2.32
566 594 1.578023 CGTGCGTAGACTCGACAATTC 59.422 52.381 0.00 0.00 0.00 2.17
568 596 0.566593 GCGTAGACTCGACAATTCGC 59.433 55.000 0.00 0.00 45.46 4.70
569 597 1.189403 CGTAGACTCGACAATTCGCC 58.811 55.000 0.00 0.00 45.46 5.54
570 598 1.189403 GTAGACTCGACAATTCGCCG 58.811 55.000 0.00 0.00 45.46 6.46
571 599 0.524816 TAGACTCGACAATTCGCCGC 60.525 55.000 0.00 0.00 45.46 6.53
572 600 2.048597 ACTCGACAATTCGCCGCA 60.049 55.556 0.00 0.00 45.46 5.69
573 601 1.421410 GACTCGACAATTCGCCGCAT 61.421 55.000 0.00 0.00 45.46 4.73
574 602 1.019278 ACTCGACAATTCGCCGCATT 61.019 50.000 0.00 0.00 45.46 3.56
575 603 0.587242 CTCGACAATTCGCCGCATTG 60.587 55.000 7.91 7.91 45.46 2.82
576 604 2.216920 CGACAATTCGCCGCATTGC 61.217 57.895 9.35 0.00 38.71 3.56
577 605 1.137404 GACAATTCGCCGCATTGCT 59.863 52.632 9.35 0.00 35.36 3.91
578 606 1.135699 GACAATTCGCCGCATTGCTG 61.136 55.000 9.35 0.83 35.36 4.41
579 607 1.874915 CAATTCGCCGCATTGCTGG 60.875 57.895 7.12 10.65 0.00 4.85
580 608 2.045708 AATTCGCCGCATTGCTGGA 61.046 52.632 19.24 6.42 0.00 3.86
581 609 1.996786 AATTCGCCGCATTGCTGGAG 61.997 55.000 19.24 16.49 0.00 3.86
584 612 2.751436 GCCGCATTGCTGGAGGAA 60.751 61.111 19.24 0.00 0.00 3.36
585 613 2.342650 GCCGCATTGCTGGAGGAAA 61.343 57.895 19.24 0.00 0.00 3.13
586 614 1.876497 GCCGCATTGCTGGAGGAAAA 61.876 55.000 19.24 0.00 0.00 2.29
587 615 0.171903 CCGCATTGCTGGAGGAAAAG 59.828 55.000 12.34 0.00 0.00 2.27
588 616 1.167851 CGCATTGCTGGAGGAAAAGA 58.832 50.000 7.12 0.00 0.00 2.52
589 617 1.541147 CGCATTGCTGGAGGAAAAGAA 59.459 47.619 7.12 0.00 0.00 2.52
590 618 2.030007 CGCATTGCTGGAGGAAAAGAAA 60.030 45.455 7.12 0.00 0.00 2.52
591 619 3.552684 CGCATTGCTGGAGGAAAAGAAAA 60.553 43.478 7.12 0.00 0.00 2.29
592 620 4.379652 GCATTGCTGGAGGAAAAGAAAAA 58.620 39.130 0.16 0.00 0.00 1.94
651 679 3.942539 AAAAAGACAATTTGCCGCAAC 57.057 38.095 4.98 0.00 0.00 4.17
652 680 1.864565 AAAGACAATTTGCCGCAACC 58.135 45.000 4.98 0.00 0.00 3.77
653 681 0.749649 AAGACAATTTGCCGCAACCA 59.250 45.000 4.98 0.00 0.00 3.67
654 682 0.314935 AGACAATTTGCCGCAACCAG 59.685 50.000 4.98 0.87 0.00 4.00
655 683 1.284297 GACAATTTGCCGCAACCAGC 61.284 55.000 4.98 0.00 40.87 4.85
743 771 0.462759 AGTAGCCAGGATTTCAGCGC 60.463 55.000 0.00 0.00 0.00 5.92
759 787 4.486503 GCAGGGCTCTGGCTGGAG 62.487 72.222 17.16 4.20 41.19 3.86
762 790 4.154347 GGGCTCTGGCTGGAGTCG 62.154 72.222 9.11 0.00 38.69 4.18
885 913 2.464459 CCTCGGCTTGATTCACCGC 61.464 63.158 10.09 5.02 46.49 5.68
886 914 1.448540 CTCGGCTTGATTCACCGCT 60.449 57.895 10.09 0.00 46.49 5.52
887 915 1.424493 CTCGGCTTGATTCACCGCTC 61.424 60.000 10.09 0.32 46.49 5.03
888 916 2.464459 CGGCTTGATTCACCGCTCC 61.464 63.158 3.13 0.00 40.55 4.70
889 917 2.115291 GGCTTGATTCACCGCTCCC 61.115 63.158 6.97 0.00 0.00 4.30
890 918 2.115291 GCTTGATTCACCGCTCCCC 61.115 63.158 0.00 0.00 0.00 4.81
891 919 1.452108 CTTGATTCACCGCTCCCCC 60.452 63.158 0.00 0.00 0.00 5.40
892 920 1.915078 CTTGATTCACCGCTCCCCCT 61.915 60.000 0.00 0.00 0.00 4.79
895 923 3.943137 ATTCACCGCTCCCCCTCCA 62.943 63.158 0.00 0.00 0.00 3.86
901 929 4.741239 GCTCCCCCTCCACCTCCA 62.741 72.222 0.00 0.00 0.00 3.86
919 947 4.547367 CCCGGACCCGCAAGATCC 62.547 72.222 0.73 0.00 43.02 3.36
921 949 4.891727 CGGACCCGCAAGATCCCG 62.892 72.222 0.00 0.00 43.02 5.14
924 952 3.735037 GACCCGCAAGATCCCGACC 62.735 68.421 0.00 0.00 43.02 4.79
925 953 4.547367 CCCGCAAGATCCCGACCC 62.547 72.222 0.00 0.00 43.02 4.46
926 954 4.891727 CCGCAAGATCCCGACCCG 62.892 72.222 0.00 0.00 43.02 5.28
929 957 4.891727 CAAGATCCCGACCCGCCG 62.892 72.222 0.00 0.00 0.00 6.46
984 1012 4.778143 CCGGGTGGGCGGAAGAAG 62.778 72.222 0.00 0.00 0.00 2.85
1153 1203 1.309102 CCCTCCCATCCCCCTCTTT 60.309 63.158 0.00 0.00 0.00 2.52
1155 1205 0.327964 CCTCCCATCCCCCTCTTTCT 60.328 60.000 0.00 0.00 0.00 2.52
1171 1221 2.561733 TTCTGATTCGCTCGATTCGT 57.438 45.000 5.89 0.00 0.00 3.85
1179 1229 3.902063 CTCGATTCGTGCGTGGCG 61.902 66.667 5.89 0.00 0.00 5.69
1221 1271 4.856607 GGAGGCGCCGTTCTCGAG 62.857 72.222 23.20 5.93 39.71 4.04
1258 1308 1.153628 CGGCCTTCGATTCGGTTCT 60.154 57.895 6.18 0.00 42.43 3.01
1259 1309 1.146358 CGGCCTTCGATTCGGTTCTC 61.146 60.000 6.18 0.00 42.43 2.87
1272 1332 1.403514 CGGTTCTCTTCTGCTCTGTCC 60.404 57.143 0.00 0.00 0.00 4.02
1355 1416 0.179150 CTCGCCGAGTTCTTCCTCTG 60.179 60.000 5.82 0.00 0.00 3.35
1361 1422 2.094649 CCGAGTTCTTCCTCTGGTACAC 60.095 54.545 0.00 0.00 0.00 2.90
1363 1424 4.008330 CGAGTTCTTCCTCTGGTACACTA 58.992 47.826 0.00 0.00 0.00 2.74
1510 1594 6.208797 TGGATTAGGTACTAGATGTTGATCCG 59.791 42.308 0.00 0.00 44.25 4.18
1526 1611 1.374252 CCGTGACCAAGAGAACCGG 60.374 63.158 0.00 0.00 0.00 5.28
1579 1664 2.615869 CTGCTGTCTCCTTGTTCTAGC 58.384 52.381 0.00 0.00 0.00 3.42
1686 1775 7.987458 TCATTTACATAGTCAGATGGTCTTTCC 59.013 37.037 0.00 0.00 0.00 3.13
1702 1791 3.329814 TCTTTCCAGAGTACTTTTCCCCC 59.670 47.826 0.00 0.00 0.00 5.40
1783 1894 5.388682 CGAATATTGGCAGCAACAAAAACAG 60.389 40.000 0.00 0.00 0.00 3.16
1811 1922 4.081406 CCATCCTCACTGAATGACCAAAA 58.919 43.478 0.00 0.00 32.37 2.44
1818 1929 6.317789 TCACTGAATGACCAAAAGATGAAC 57.682 37.500 0.00 0.00 29.99 3.18
1827 1938 3.019564 CCAAAAGATGAACCCCTAGCTG 58.980 50.000 0.00 0.00 0.00 4.24
1844 1955 3.221771 AGCTGACCTAGATCTAGCACAG 58.778 50.000 29.50 29.50 37.59 3.66
1845 1956 2.288152 GCTGACCTAGATCTAGCACAGC 60.288 54.545 35.24 35.24 44.38 4.40
1863 1974 2.886523 CAGCATGAGAACAAAGGAACCA 59.113 45.455 0.00 0.00 39.69 3.67
1870 3489 2.040412 AGAACAAAGGAACCAGGCCTAG 59.960 50.000 3.98 0.00 33.76 3.02
1871 3490 1.446016 ACAAAGGAACCAGGCCTAGT 58.554 50.000 3.98 0.00 33.76 2.57
1877 3496 2.124507 GAACCAGGCCTAGTGCACCA 62.125 60.000 14.63 0.00 43.89 4.17
1878 3497 2.129555 AACCAGGCCTAGTGCACCAG 62.130 60.000 14.63 9.67 43.89 4.00
1933 3552 1.767759 AGCTCACAACCAAACTGCTT 58.232 45.000 0.00 0.00 0.00 3.91
1937 3556 2.684881 CTCACAACCAAACTGCTTCTGT 59.315 45.455 0.00 0.00 0.00 3.41
1938 3557 2.423185 TCACAACCAAACTGCTTCTGTG 59.577 45.455 0.00 0.00 35.21 3.66
1964 3583 1.381872 AGGGACATGACCTCCGAGG 60.382 63.158 13.31 13.31 42.49 4.63
1975 3594 2.002505 CCTCCGAGGTATGAGTGGAT 57.997 55.000 6.24 0.00 0.00 3.41
1977 3596 1.000283 CTCCGAGGTATGAGTGGATGC 60.000 57.143 0.00 0.00 0.00 3.91
2001 3623 0.249073 CCCGTGTAGGCAGATCTTCG 60.249 60.000 0.00 0.00 39.21 3.79
2028 3650 3.435890 GCCTAGGATCAGAGTAGGTGAGT 60.436 52.174 14.75 0.00 36.46 3.41
2035 3657 1.671845 CAGAGTAGGTGAGTAGACGCC 59.328 57.143 0.00 0.00 40.34 5.68
2037 3659 0.747283 AGTAGGTGAGTAGACGCCGG 60.747 60.000 0.00 0.00 44.16 6.13
2045 3667 2.357760 TAGACGCCGGCAAACACC 60.358 61.111 28.98 7.91 0.00 4.16
2061 3683 1.968017 ACCCATTGCAGCGACAGTG 60.968 57.895 0.00 0.00 0.00 3.66
2065 3687 0.110056 CATTGCAGCGACAGTGAACC 60.110 55.000 0.00 0.00 29.31 3.62
2066 3688 0.250467 ATTGCAGCGACAGTGAACCT 60.250 50.000 0.00 0.00 0.00 3.50
2110 3732 0.835941 ATTGCGAAGAGGAGGAGCAT 59.164 50.000 0.00 0.00 37.68 3.79
2111 3733 0.107993 TTGCGAAGAGGAGGAGCATG 60.108 55.000 0.00 0.00 37.68 4.06
2131 3753 1.610624 GGGGCTTCAAAGATCGTGTCA 60.611 52.381 0.00 0.00 0.00 3.58
2133 3755 1.126846 GGCTTCAAAGATCGTGTCACG 59.873 52.381 19.38 19.38 44.19 4.35
2158 3780 2.802724 GCCCCACACCCCAAAACAC 61.803 63.158 0.00 0.00 0.00 3.32
2179 3801 3.444388 ACAACCGTGTAACCAACATTTGT 59.556 39.130 0.00 0.00 41.10 2.83
2181 3803 3.280295 ACCGTGTAACCAACATTTGTCA 58.720 40.909 0.00 0.00 41.10 3.58
2186 3808 5.007823 CGTGTAACCAACATTTGTCACCTTA 59.992 40.000 0.00 0.00 41.10 2.69
2191 3813 7.648039 AACCAACATTTGTCACCTTAGTTAA 57.352 32.000 0.00 0.00 0.00 2.01
2193 3815 6.831868 ACCAACATTTGTCACCTTAGTTAAGT 59.168 34.615 0.00 0.00 0.00 2.24
2201 3823 9.781633 TTTGTCACCTTAGTTAAGTATAAAGCA 57.218 29.630 0.00 0.00 0.00 3.91
2249 3871 3.309296 CCCTCTCTGTTATCTGGGCTTA 58.691 50.000 0.00 0.00 0.00 3.09
2253 3876 5.994668 CCTCTCTGTTATCTGGGCTTATTTC 59.005 44.000 0.00 0.00 0.00 2.17
2254 3877 6.408548 CCTCTCTGTTATCTGGGCTTATTTCA 60.409 42.308 0.00 0.00 0.00 2.69
2263 3886 7.756395 ATCTGGGCTTATTTCAGTTATCATG 57.244 36.000 0.00 0.00 0.00 3.07
2349 3972 2.525368 TGTCAGCTGACTAGGCAGTTA 58.475 47.619 38.81 18.86 44.99 2.24
2356 3979 4.010349 GCTGACTAGGCAGTTAATTGGTT 58.990 43.478 26.42 0.00 38.17 3.67
2367 3990 5.416013 GCAGTTAATTGGTTCTAGCTTCCTT 59.584 40.000 0.00 0.00 0.00 3.36
2395 4021 6.725834 CCCCTTAATTATATGCATCCCTGTTT 59.274 38.462 0.19 0.00 0.00 2.83
2482 4112 6.152492 TGCAGTCATGTTTTTATGCCATTCTA 59.848 34.615 0.00 0.00 32.77 2.10
2506 4136 3.073228 TCCACTGGGACTTCTCCTG 57.927 57.895 0.00 0.00 38.64 3.86
2509 4139 3.871623 ACTGGGACTTCTCCTGTGA 57.128 52.632 0.00 0.00 36.68 3.58
2510 4140 2.334006 ACTGGGACTTCTCCTGTGAT 57.666 50.000 0.00 0.00 36.68 3.06
2511 4141 1.905215 ACTGGGACTTCTCCTGTGATG 59.095 52.381 0.00 0.00 36.68 3.07
2533 4165 5.486526 TGTCTGTTTTGGTTCTGCAAAAAT 58.513 33.333 0.00 0.00 33.05 1.82
2627 4259 3.065925 GCCTTTGCTTCAATAGGCTAGTG 59.934 47.826 15.47 15.47 40.70 2.74
2784 4417 7.552687 AGTTGAGCTGATTTTGATTTCCGTATA 59.447 33.333 0.00 0.00 0.00 1.47
2918 4551 5.007430 CACATATGTTGGATCAGCTGAAGAC 59.993 44.000 22.50 16.22 0.00 3.01
3042 4675 9.421806 GATCAGTCAAGTCCAATATCTTCATAG 57.578 37.037 0.00 0.00 0.00 2.23
3046 4679 7.126421 AGTCAAGTCCAATATCTTCATAGTGGT 59.874 37.037 8.03 0.00 46.67 4.16
3092 4725 6.033196 GCACAGTTTCAAATCTTCATTCATCG 59.967 38.462 0.00 0.00 0.00 3.84
3116 4749 7.646130 TCGCACTATTTTTCCTTTTGTTACTTG 59.354 33.333 0.00 0.00 0.00 3.16
3217 4851 3.933332 GGACCCTTTGAAGATACGTGAAG 59.067 47.826 0.00 0.00 0.00 3.02
3246 4880 3.349006 GGTGTCACCGTGCTGCTG 61.349 66.667 6.18 0.00 0.00 4.41
3303 4937 5.837829 AGGGTGGGTTATTATGTGAACAAT 58.162 37.500 0.00 0.00 0.00 2.71
3339 4973 3.087666 GCTGAGAGAAGAGCCCCCG 62.088 68.421 0.00 0.00 0.00 5.73
3381 5015 2.036346 GGTGCAGAGAAACATTTTGGCT 59.964 45.455 0.00 0.00 0.00 4.75
3408 5042 1.147376 CCGTGTCACCAAGTTCCCA 59.853 57.895 0.00 0.00 0.00 4.37
3439 5073 2.345244 CTGAACCTGGCACGAGCT 59.655 61.111 4.48 0.00 41.70 4.09
3453 5087 1.669115 GAGCTCAGAACAGCCGCAA 60.669 57.895 9.40 0.00 40.65 4.85
3537 5171 2.634940 ACATATGGCGCCACTAGAGAAT 59.365 45.455 35.50 16.50 0.00 2.40
3643 5295 0.249868 CGAGAGTGGTGGTTCTGCAA 60.250 55.000 0.00 0.00 0.00 4.08
3664 5316 6.484977 TGCAATGTACTGATCTGTTGTTTACA 59.515 34.615 10.76 8.86 34.95 2.41
3804 5456 5.657949 AACCGTCGAATTGGTTACCGACA 62.658 47.826 14.37 0.00 46.34 4.35
3921 5574 7.072177 TCCGCTTTATTTCAGATAAACAGTG 57.928 36.000 0.00 0.00 0.00 3.66
3979 5632 7.556844 TCTACTGAGACTGAATATTTTGGTCC 58.443 38.462 10.60 0.00 0.00 4.46
4152 5815 3.634910 GGCTGAACCTTTTGTCCTGTTTA 59.365 43.478 0.00 0.00 34.51 2.01
4325 5991 1.577922 CTTGCGTGCACAGCTGAAT 59.422 52.632 23.35 0.00 35.28 2.57
4366 6032 6.101442 AGTGTCCTAGACCATCTAAGCTACTA 59.899 42.308 0.00 0.00 0.00 1.82
4367 6033 6.205270 GTGTCCTAGACCATCTAAGCTACTAC 59.795 46.154 0.00 0.00 0.00 2.73
4368 6034 6.126565 TGTCCTAGACCATCTAAGCTACTACA 60.127 42.308 0.00 0.00 0.00 2.74
4369 6035 6.943718 GTCCTAGACCATCTAAGCTACTACAT 59.056 42.308 0.00 0.00 0.00 2.29
4370 6036 7.120138 GTCCTAGACCATCTAAGCTACTACATC 59.880 44.444 0.00 0.00 0.00 3.06
4440 6111 4.002906 TCAAATCTAAACTGCTCACGGT 57.997 40.909 0.00 0.00 36.79 4.83
4451 6125 1.272490 TGCTCACGGTTACTTCCAGAG 59.728 52.381 0.00 0.00 34.51 3.35
4452 6126 1.997669 CTCACGGTTACTTCCAGAGC 58.002 55.000 0.00 0.00 0.00 4.09
4453 6127 1.272490 CTCACGGTTACTTCCAGAGCA 59.728 52.381 0.00 0.00 0.00 4.26
4464 6138 4.605183 ACTTCCAGAGCAGTAGTACATCT 58.395 43.478 2.52 0.25 0.00 2.90
4486 6160 7.387265 TCTAATGGTGGAGGCTTTATATTCA 57.613 36.000 0.00 0.00 0.00 2.57
4501 6175 1.176527 ATTCACTGATTGCCAACCCG 58.823 50.000 0.00 0.00 0.00 5.28
4506 6180 1.303970 TGATTGCCAACCCGCATCA 60.304 52.632 0.00 0.00 38.87 3.07
4516 6190 1.626686 ACCCGCATCAACCATTGAAA 58.373 45.000 0.00 0.00 43.95 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.672673 TTCTCATTTTCAATTTTTGGGTGTAAA 57.327 25.926 0.00 0.00 0.00 2.01
115 119 6.670452 GCAAAATCAAAGTACATGGAATTGCG 60.670 38.462 11.32 0.00 0.00 4.85
194 199 8.147642 ACATTTAAAATTCCAAAAATGTCGCA 57.852 26.923 6.48 0.00 44.91 5.10
348 376 8.693542 AGTTTTCTTTCATTTCTCAACAACTG 57.306 30.769 0.00 0.00 0.00 3.16
412 440 5.896073 TCTTCCCTGTTTCTTTTCTCTCT 57.104 39.130 0.00 0.00 0.00 3.10
414 442 6.253946 TCTTCTTCCCTGTTTCTTTTCTCT 57.746 37.500 0.00 0.00 0.00 3.10
415 443 6.944234 TTCTTCTTCCCTGTTTCTTTTCTC 57.056 37.500 0.00 0.00 0.00 2.87
416 444 7.718334 TTTTCTTCTTCCCTGTTTCTTTTCT 57.282 32.000 0.00 0.00 0.00 2.52
417 445 7.009265 CGTTTTTCTTCTTCCCTGTTTCTTTTC 59.991 37.037 0.00 0.00 0.00 2.29
418 446 6.811665 CGTTTTTCTTCTTCCCTGTTTCTTTT 59.188 34.615 0.00 0.00 0.00 2.27
473 501 0.397957 AGGTTTCCAGCCGGGTTTTT 60.398 50.000 1.64 0.00 38.11 1.94
474 502 0.826256 GAGGTTTCCAGCCGGGTTTT 60.826 55.000 1.64 0.00 38.11 2.43
475 503 1.228459 GAGGTTTCCAGCCGGGTTT 60.228 57.895 1.64 0.00 38.11 3.27
476 504 2.434774 GAGGTTTCCAGCCGGGTT 59.565 61.111 1.64 0.00 38.11 4.11
477 505 3.647771 GGAGGTTTCCAGCCGGGT 61.648 66.667 0.00 0.00 43.45 5.28
478 506 4.778143 CGGAGGTTTCCAGCCGGG 62.778 72.222 2.18 0.00 44.26 5.73
479 507 3.248446 TTCGGAGGTTTCCAGCCGG 62.248 63.158 15.85 0.00 44.26 6.13
480 508 1.741770 CTTCGGAGGTTTCCAGCCG 60.742 63.158 11.79 11.79 44.26 5.52
481 509 1.377333 CCTTCGGAGGTTTCCAGCC 60.377 63.158 0.00 0.00 44.26 4.85
482 510 4.303257 CCTTCGGAGGTTTCCAGC 57.697 61.111 0.00 0.00 44.26 4.85
499 527 1.153429 CGATCCGGGTTCTGGGAAC 60.153 63.158 0.00 2.19 35.60 3.62
500 528 3.026431 GCGATCCGGGTTCTGGGAA 62.026 63.158 0.00 0.00 35.60 3.97
501 529 3.467226 GCGATCCGGGTTCTGGGA 61.467 66.667 0.00 0.00 36.61 4.37
502 530 3.447025 GAGCGATCCGGGTTCTGGG 62.447 68.421 0.00 0.00 0.00 4.45
503 531 2.107141 GAGCGATCCGGGTTCTGG 59.893 66.667 0.00 0.00 0.00 3.86
504 532 0.391130 TTTGAGCGATCCGGGTTCTG 60.391 55.000 0.00 0.00 0.00 3.02
505 533 0.391263 GTTTGAGCGATCCGGGTTCT 60.391 55.000 0.00 0.00 0.00 3.01
506 534 1.693083 CGTTTGAGCGATCCGGGTTC 61.693 60.000 0.00 0.00 0.00 3.62
507 535 1.740296 CGTTTGAGCGATCCGGGTT 60.740 57.895 0.00 0.00 0.00 4.11
508 536 2.125673 CGTTTGAGCGATCCGGGT 60.126 61.111 0.00 0.00 0.00 5.28
509 537 3.564027 GCGTTTGAGCGATCCGGG 61.564 66.667 0.00 0.00 0.00 5.73
510 538 2.509336 AGCGTTTGAGCGATCCGG 60.509 61.111 0.00 0.00 43.00 5.14
511 539 2.849966 CGAGCGTTTGAGCGATCCG 61.850 63.158 0.00 0.00 43.34 4.18
512 540 2.998667 CGAGCGTTTGAGCGATCC 59.001 61.111 0.00 0.00 43.34 3.36
513 541 2.072038 GAGCGAGCGTTTGAGCGATC 62.072 60.000 0.00 0.00 42.90 3.69
514 542 2.125912 AGCGAGCGTTTGAGCGAT 60.126 55.556 0.00 0.00 43.00 4.58
515 543 2.749110 AAGAGCGAGCGTTTGAGCGA 62.749 55.000 0.00 0.00 43.00 4.93
516 544 2.272293 GAAGAGCGAGCGTTTGAGCG 62.272 60.000 0.00 0.00 43.00 5.03
517 545 1.011451 AGAAGAGCGAGCGTTTGAGC 61.011 55.000 0.00 0.00 37.41 4.26
518 546 0.988439 GAGAAGAGCGAGCGTTTGAG 59.012 55.000 0.00 0.00 0.00 3.02
519 547 0.598562 AGAGAAGAGCGAGCGTTTGA 59.401 50.000 0.00 0.00 0.00 2.69
520 548 0.712775 CAGAGAAGAGCGAGCGTTTG 59.287 55.000 0.00 0.00 0.00 2.93
521 549 1.011451 GCAGAGAAGAGCGAGCGTTT 61.011 55.000 0.00 0.00 0.00 3.60
522 550 1.445238 GCAGAGAAGAGCGAGCGTT 60.445 57.895 0.00 0.00 0.00 4.84
523 551 2.180518 GCAGAGAAGAGCGAGCGT 59.819 61.111 0.00 0.00 0.00 5.07
524 552 2.581953 GGCAGAGAAGAGCGAGCG 60.582 66.667 0.00 0.00 0.00 5.03
525 553 1.519013 CAGGCAGAGAAGAGCGAGC 60.519 63.158 0.00 0.00 0.00 5.03
526 554 0.458197 CACAGGCAGAGAAGAGCGAG 60.458 60.000 0.00 0.00 0.00 5.03
527 555 1.588597 CACAGGCAGAGAAGAGCGA 59.411 57.895 0.00 0.00 0.00 4.93
528 556 2.099431 GCACAGGCAGAGAAGAGCG 61.099 63.158 0.00 0.00 40.72 5.03
529 557 2.099431 CGCACAGGCAGAGAAGAGC 61.099 63.158 0.00 0.00 41.24 4.09
530 558 1.013005 CACGCACAGGCAGAGAAGAG 61.013 60.000 0.00 0.00 41.24 2.85
531 559 1.005748 CACGCACAGGCAGAGAAGA 60.006 57.895 0.00 0.00 41.24 2.87
532 560 2.675056 GCACGCACAGGCAGAGAAG 61.675 63.158 0.00 0.00 41.24 2.85
533 561 2.666190 GCACGCACAGGCAGAGAA 60.666 61.111 0.00 0.00 41.24 2.87
535 563 3.914605 TACGCACGCACAGGCAGAG 62.915 63.158 0.00 0.00 41.24 3.35
536 564 3.914605 CTACGCACGCACAGGCAGA 62.915 63.158 0.00 0.00 41.24 4.26
537 565 3.481903 CTACGCACGCACAGGCAG 61.482 66.667 0.00 0.00 41.24 4.85
538 566 3.984749 TCTACGCACGCACAGGCA 61.985 61.111 0.00 0.00 41.24 4.75
539 567 3.479269 GTCTACGCACGCACAGGC 61.479 66.667 0.00 0.00 0.00 4.85
540 568 1.801913 GAGTCTACGCACGCACAGG 60.802 63.158 0.00 0.00 0.00 4.00
541 569 2.146519 CGAGTCTACGCACGCACAG 61.147 63.158 0.00 0.00 0.00 3.66
542 570 2.127003 CGAGTCTACGCACGCACA 60.127 61.111 0.00 0.00 0.00 4.57
543 571 2.144680 GTCGAGTCTACGCACGCAC 61.145 63.158 0.00 0.00 0.00 5.34
544 572 2.120355 TTGTCGAGTCTACGCACGCA 62.120 55.000 0.00 0.00 0.00 5.24
545 573 0.797249 ATTGTCGAGTCTACGCACGC 60.797 55.000 0.00 0.00 0.00 5.34
546 574 1.578023 GAATTGTCGAGTCTACGCACG 59.422 52.381 0.00 0.00 0.00 5.34
559 587 1.135699 CAGCAATGCGGCGAATTGTC 61.136 55.000 34.16 26.81 37.35 3.18
560 588 1.153978 CAGCAATGCGGCGAATTGT 60.154 52.632 34.16 21.54 37.35 2.71
561 589 1.874915 CCAGCAATGCGGCGAATTG 60.875 57.895 31.49 31.49 39.27 2.32
562 590 1.996786 CTCCAGCAATGCGGCGAATT 61.997 55.000 12.98 10.00 39.27 2.17
563 591 2.438254 TCCAGCAATGCGGCGAAT 60.438 55.556 12.98 0.87 39.27 3.34
564 592 3.126879 CTCCAGCAATGCGGCGAA 61.127 61.111 12.98 0.00 39.27 4.70
567 595 1.876497 TTTTCCTCCAGCAATGCGGC 61.876 55.000 10.43 0.00 0.00 6.53
568 596 0.171903 CTTTTCCTCCAGCAATGCGG 59.828 55.000 9.27 9.27 0.00 5.69
569 597 1.167851 TCTTTTCCTCCAGCAATGCG 58.832 50.000 0.00 0.00 0.00 4.73
570 598 3.665745 TTTCTTTTCCTCCAGCAATGC 57.334 42.857 0.00 0.00 0.00 3.56
631 659 2.611751 GGTTGCGGCAAATTGTCTTTTT 59.388 40.909 18.23 0.00 0.00 1.94
632 660 2.209273 GGTTGCGGCAAATTGTCTTTT 58.791 42.857 18.23 0.00 0.00 2.27
633 661 1.137872 TGGTTGCGGCAAATTGTCTTT 59.862 42.857 18.23 0.00 0.00 2.52
634 662 0.749649 TGGTTGCGGCAAATTGTCTT 59.250 45.000 18.23 0.00 0.00 3.01
635 663 0.314935 CTGGTTGCGGCAAATTGTCT 59.685 50.000 18.23 0.00 0.00 3.41
636 664 1.284297 GCTGGTTGCGGCAAATTGTC 61.284 55.000 18.23 4.28 0.00 3.18
637 665 1.300853 GCTGGTTGCGGCAAATTGT 60.301 52.632 18.23 0.00 0.00 2.71
638 666 3.553039 GCTGGTTGCGGCAAATTG 58.447 55.556 18.23 10.86 0.00 2.32
647 675 1.139520 CCTATTTGCCGCTGGTTGC 59.860 57.895 0.00 0.00 38.57 4.17
648 676 1.666209 CCCCTATTTGCCGCTGGTTG 61.666 60.000 0.00 0.00 0.00 3.77
649 677 1.379843 CCCCTATTTGCCGCTGGTT 60.380 57.895 0.00 0.00 0.00 3.67
650 678 2.150014 AACCCCTATTTGCCGCTGGT 62.150 55.000 0.00 0.00 0.00 4.00
651 679 0.970427 AAACCCCTATTTGCCGCTGG 60.970 55.000 0.00 0.00 0.00 4.85
652 680 0.455815 GAAACCCCTATTTGCCGCTG 59.544 55.000 0.00 0.00 0.00 5.18
653 681 0.683179 GGAAACCCCTATTTGCCGCT 60.683 55.000 0.00 0.00 0.00 5.52
654 682 1.813859 GGAAACCCCTATTTGCCGC 59.186 57.895 0.00 0.00 0.00 6.53
655 683 0.393267 TCGGAAACCCCTATTTGCCG 60.393 55.000 0.00 0.00 35.44 5.69
656 684 1.389555 CTCGGAAACCCCTATTTGCC 58.610 55.000 0.00 0.00 0.00 4.52
657 685 0.738975 GCTCGGAAACCCCTATTTGC 59.261 55.000 0.00 0.00 0.00 3.68
658 686 1.389555 GGCTCGGAAACCCCTATTTG 58.610 55.000 0.00 0.00 0.00 2.32
659 687 0.107361 CGGCTCGGAAACCCCTATTT 60.107 55.000 0.00 0.00 0.00 1.40
660 688 1.525442 CGGCTCGGAAACCCCTATT 59.475 57.895 0.00 0.00 0.00 1.73
661 689 3.103091 GCGGCTCGGAAACCCCTAT 62.103 63.158 0.00 0.00 0.00 2.57
682 710 2.774351 GCTCCCCTGCCCACCTAT 60.774 66.667 0.00 0.00 0.00 2.57
743 771 3.007920 ACTCCAGCCAGAGCCCTG 61.008 66.667 0.58 0.00 41.25 4.45
749 777 2.604686 AAGCCGACTCCAGCCAGA 60.605 61.111 0.00 0.00 0.00 3.86
750 778 2.125350 GAAGCCGACTCCAGCCAG 60.125 66.667 0.00 0.00 0.00 4.85
751 779 3.706373 GGAAGCCGACTCCAGCCA 61.706 66.667 0.00 0.00 0.00 4.75
752 780 4.475135 GGGAAGCCGACTCCAGCC 62.475 72.222 0.00 0.00 0.00 4.85
753 781 4.475135 GGGGAAGCCGACTCCAGC 62.475 72.222 0.00 0.00 0.00 4.85
754 782 4.148825 CGGGGAAGCCGACTCCAG 62.149 72.222 0.00 0.00 0.00 3.86
756 784 4.452733 CACGGGGAAGCCGACTCC 62.453 72.222 0.00 0.00 34.52 3.85
829 857 2.063015 TTTTTGGAGGAGGGAGCGCA 62.063 55.000 11.47 0.00 0.00 6.09
858 886 2.685380 AAGCCGAGGGAGGAGTGG 60.685 66.667 0.00 0.00 0.00 4.00
859 887 1.333636 ATCAAGCCGAGGGAGGAGTG 61.334 60.000 0.00 0.00 0.00 3.51
860 888 0.618968 AATCAAGCCGAGGGAGGAGT 60.619 55.000 0.00 0.00 0.00 3.85
861 889 0.105778 GAATCAAGCCGAGGGAGGAG 59.894 60.000 0.00 0.00 0.00 3.69
862 890 0.617535 TGAATCAAGCCGAGGGAGGA 60.618 55.000 0.00 0.00 0.00 3.71
863 891 0.462759 GTGAATCAAGCCGAGGGAGG 60.463 60.000 0.00 0.00 0.00 4.30
864 892 0.462759 GGTGAATCAAGCCGAGGGAG 60.463 60.000 0.00 0.00 0.00 4.30
865 893 1.602237 GGTGAATCAAGCCGAGGGA 59.398 57.895 0.00 0.00 0.00 4.20
866 894 4.225497 GGTGAATCAAGCCGAGGG 57.775 61.111 0.00 0.00 0.00 4.30
871 899 2.115291 GGGAGCGGTGAATCAAGCC 61.115 63.158 8.07 0.00 0.00 4.35
872 900 2.115291 GGGGAGCGGTGAATCAAGC 61.115 63.158 0.00 4.16 0.00 4.01
873 901 1.452108 GGGGGAGCGGTGAATCAAG 60.452 63.158 0.00 0.00 0.00 3.02
884 912 4.741239 TGGAGGTGGAGGGGGAGC 62.741 72.222 0.00 0.00 0.00 4.70
885 913 2.689034 GTGGAGGTGGAGGGGGAG 60.689 72.222 0.00 0.00 0.00 4.30
886 914 4.348495 GGTGGAGGTGGAGGGGGA 62.348 72.222 0.00 0.00 0.00 4.81
890 918 4.715130 TCCGGGTGGAGGTGGAGG 62.715 72.222 0.00 0.00 40.17 4.30
901 929 3.782443 GATCTTGCGGGTCCGGGT 61.782 66.667 11.60 0.00 40.19 5.28
934 962 2.565645 AATCGATCGAGGAGCGGGG 61.566 63.158 23.84 0.00 41.96 5.73
935 963 1.372251 CAATCGATCGAGGAGCGGG 60.372 63.158 23.84 3.78 41.96 6.13
936 964 0.242286 ATCAATCGATCGAGGAGCGG 59.758 55.000 23.84 8.73 41.96 5.52
937 965 2.902065 TATCAATCGATCGAGGAGCG 57.098 50.000 23.84 9.47 43.08 5.03
938 966 4.095632 TCTGATATCAATCGATCGAGGAGC 59.904 45.833 23.84 15.36 34.60 4.70
939 967 5.568482 GTCTGATATCAATCGATCGAGGAG 58.432 45.833 23.84 14.88 34.60 3.69
1137 1165 0.842635 CAGAAAGAGGGGGATGGGAG 59.157 60.000 0.00 0.00 0.00 4.30
1142 1170 1.141858 GCGAATCAGAAAGAGGGGGAT 59.858 52.381 0.00 0.00 0.00 3.85
1145 1173 1.804372 CGAGCGAATCAGAAAGAGGGG 60.804 57.143 0.00 0.00 0.00 4.79
1153 1203 1.827578 CACGAATCGAGCGAATCAGA 58.172 50.000 10.55 0.00 0.00 3.27
1155 1205 2.288013 GCACGAATCGAGCGAATCA 58.712 52.632 10.55 0.00 33.66 2.57
1186 1236 2.928116 CTCCTAAAACGAAACCCTAGCG 59.072 50.000 0.00 0.00 0.00 4.26
1249 1299 2.564947 ACAGAGCAGAAGAGAACCGAAT 59.435 45.455 0.00 0.00 0.00 3.34
1258 1308 0.616111 GGAGGGGACAGAGCAGAAGA 60.616 60.000 0.00 0.00 0.00 2.87
1259 1309 0.906756 TGGAGGGGACAGAGCAGAAG 60.907 60.000 0.00 0.00 0.00 2.85
1345 1405 5.580998 AGATGTAGTGTACCAGAGGAAGAA 58.419 41.667 0.00 0.00 0.00 2.52
1355 1416 2.953466 TCGCCAAGATGTAGTGTACC 57.047 50.000 0.00 0.00 0.00 3.34
1361 1422 2.938451 TGCAGAAATCGCCAAGATGTAG 59.062 45.455 0.00 0.00 40.02 2.74
1363 1424 1.741706 CTGCAGAAATCGCCAAGATGT 59.258 47.619 8.42 0.00 40.02 3.06
1510 1594 2.224113 TGTAACCGGTTCTCTTGGTCAC 60.224 50.000 26.16 13.57 34.11 3.67
1526 1611 3.440522 GGCTCCACAAAATCCTCTGTAAC 59.559 47.826 0.00 0.00 0.00 2.50
1608 1696 6.327934 AGCTCAATGTAATTTCAGCATCAAC 58.672 36.000 0.00 0.00 40.53 3.18
1609 1697 6.519679 AGCTCAATGTAATTTCAGCATCAA 57.480 33.333 0.00 0.00 40.53 2.57
1610 1698 6.327154 CAAGCTCAATGTAATTTCAGCATCA 58.673 36.000 0.00 0.00 40.53 3.07
1611 1699 5.747197 CCAAGCTCAATGTAATTTCAGCATC 59.253 40.000 0.00 0.00 40.53 3.91
1612 1700 5.419788 TCCAAGCTCAATGTAATTTCAGCAT 59.580 36.000 0.00 0.00 40.53 3.79
1702 1791 3.432252 ACAAAAATTACACGCTCGAGAGG 59.568 43.478 18.75 9.62 0.00 3.69
1707 1796 7.597643 TTTCTTAACAAAAATTACACGCTCG 57.402 32.000 0.00 0.00 0.00 5.03
1738 1848 3.778718 CGTTATTCACGTTTGCACTATGC 59.221 43.478 0.00 0.00 44.49 3.14
1771 1882 4.982295 GGATGGTAGTTCTGTTTTTGTTGC 59.018 41.667 0.00 0.00 0.00 4.17
1772 1883 6.039270 TGAGGATGGTAGTTCTGTTTTTGTTG 59.961 38.462 0.00 0.00 0.00 3.33
1783 1894 5.112686 GTCATTCAGTGAGGATGGTAGTTC 58.887 45.833 5.22 0.00 37.56 3.01
1811 1922 1.008938 AGGTCAGCTAGGGGTTCATCT 59.991 52.381 0.00 0.00 0.00 2.90
1818 1929 2.990740 AGATCTAGGTCAGCTAGGGG 57.009 55.000 11.05 0.00 0.00 4.79
1827 1938 3.571828 TCATGCTGTGCTAGATCTAGGTC 59.428 47.826 27.21 14.43 33.87 3.85
1844 1955 2.229784 CCTGGTTCCTTTGTTCTCATGC 59.770 50.000 0.00 0.00 0.00 4.06
1845 1956 2.229784 GCCTGGTTCCTTTGTTCTCATG 59.770 50.000 0.00 0.00 0.00 3.07
1863 1974 1.992277 CTCCTGGTGCACTAGGCCT 60.992 63.158 37.14 11.78 43.51 5.19
1910 3529 2.099756 GCAGTTTGGTTGTGAGCTTTCT 59.900 45.455 0.00 0.00 0.00 2.52
1937 3556 0.537143 GTCATGTCCCTGTGTTGCCA 60.537 55.000 0.00 0.00 0.00 4.92
1938 3557 1.244019 GGTCATGTCCCTGTGTTGCC 61.244 60.000 0.00 0.00 0.00 4.52
1985 3607 0.175760 TGCCGAAGATCTGCCTACAC 59.824 55.000 0.00 0.00 0.00 2.90
2001 3623 1.127343 ACTCTGATCCTAGGCTTGCC 58.873 55.000 2.96 2.97 0.00 4.52
2028 3650 2.357760 GGTGTTTGCCGGCGTCTA 60.358 61.111 23.90 5.45 0.00 2.59
2035 3657 1.373246 CTGCAATGGGTGTTTGCCG 60.373 57.895 5.99 0.00 46.97 5.69
2045 3667 0.110056 GTTCACTGTCGCTGCAATGG 60.110 55.000 0.00 0.00 0.00 3.16
2061 3683 3.376918 GCTGGGCAAGGCAGGTTC 61.377 66.667 0.00 0.00 0.00 3.62
2110 3732 0.400213 ACACGATCTTTGAAGCCCCA 59.600 50.000 0.00 0.00 0.00 4.96
2111 3733 1.087501 GACACGATCTTTGAAGCCCC 58.912 55.000 0.00 0.00 0.00 5.80
2131 3753 4.388499 GTGTGGGGCATCGGTCGT 62.388 66.667 0.00 0.00 0.00 4.34
2133 3755 4.796495 GGGTGTGGGGCATCGGTC 62.796 72.222 0.00 0.00 0.00 4.79
2136 3758 3.877344 TTTGGGGTGTGGGGCATCG 62.877 63.158 0.00 0.00 0.00 3.84
2138 3760 1.841103 GTTTTGGGGTGTGGGGCAT 60.841 57.895 0.00 0.00 0.00 4.40
2158 3780 4.035278 ACAAATGTTGGTTACACGGTTG 57.965 40.909 0.00 0.00 40.19 3.77
2166 3788 8.749026 TTAACTAAGGTGACAAATGTTGGTTA 57.251 30.769 0.00 0.00 34.12 2.85
2175 3797 9.781633 TGCTTTATACTTAACTAAGGTGACAAA 57.218 29.630 1.76 0.00 37.62 2.83
2179 3801 9.211485 GTTGTGCTTTATACTTAACTAAGGTGA 57.789 33.333 1.76 0.00 37.62 4.02
2181 3803 9.563748 TTGTTGTGCTTTATACTTAACTAAGGT 57.436 29.630 1.76 0.00 37.62 3.50
2201 3823 8.911662 GCGTAATCAAACTAAATTCATTGTTGT 58.088 29.630 0.00 0.00 0.00 3.32
2249 3871 9.739276 TTAAGTGAAGGACATGATAACTGAAAT 57.261 29.630 0.00 0.00 0.00 2.17
2253 3876 8.616076 GGAATTAAGTGAAGGACATGATAACTG 58.384 37.037 0.00 0.00 0.00 3.16
2254 3877 8.552296 AGGAATTAAGTGAAGGACATGATAACT 58.448 33.333 0.00 0.00 0.00 2.24
2263 3886 7.778470 CTGTATCAGGAATTAAGTGAAGGAC 57.222 40.000 0.00 0.00 0.00 3.85
2336 3959 5.499004 AGAACCAATTAACTGCCTAGTCA 57.501 39.130 0.00 0.00 35.69 3.41
2349 3972 3.092301 GGCAAGGAAGCTAGAACCAATT 58.908 45.455 0.00 0.00 34.17 2.32
2356 3979 0.550147 AAGGGGGCAAGGAAGCTAGA 60.550 55.000 0.00 0.00 34.17 2.43
2367 3990 4.571792 GGGATGCATATAATTAAGGGGGCA 60.572 45.833 0.00 0.00 0.00 5.36
2395 4021 2.489329 GCAGGCTGCTTCACTATTTTCA 59.511 45.455 31.37 0.00 40.96 2.69
2504 4134 4.790766 GCAGAACCAAAACAGACATCACAG 60.791 45.833 0.00 0.00 0.00 3.66
2505 4135 3.066621 GCAGAACCAAAACAGACATCACA 59.933 43.478 0.00 0.00 0.00 3.58
2506 4136 3.066621 TGCAGAACCAAAACAGACATCAC 59.933 43.478 0.00 0.00 0.00 3.06
2509 4139 4.734398 TTTGCAGAACCAAAACAGACAT 57.266 36.364 0.00 0.00 32.20 3.06
2510 4140 4.527509 TTTTGCAGAACCAAAACAGACA 57.472 36.364 0.00 0.00 39.14 3.41
2511 4141 5.006649 GGATTTTTGCAGAACCAAAACAGAC 59.993 40.000 0.00 0.00 42.49 3.51
2533 4165 2.567169 CAGTCCCACACTACTGAATGGA 59.433 50.000 0.00 0.00 44.79 3.41
2627 4259 5.627499 TCTATGTTGATTGTGAGCAAACC 57.373 39.130 0.00 0.00 38.21 3.27
2918 4551 4.631377 TCAAGTTGCTGATCATAGGTTTCG 59.369 41.667 0.00 0.00 0.00 3.46
3042 4675 6.051179 AGGAATTCTAGGTTTACTGACCAC 57.949 41.667 5.23 0.00 42.35 4.16
3046 4679 5.938125 GTGCAAGGAATTCTAGGTTTACTGA 59.062 40.000 5.23 0.00 0.00 3.41
3092 4725 7.923878 TCCAAGTAACAAAAGGAAAAATAGTGC 59.076 33.333 0.00 0.00 0.00 4.40
3217 4851 2.416547 CGGTGACACCAATGATGTCTTC 59.583 50.000 24.18 2.51 45.58 2.87
3246 4880 1.359848 CCACGTAGGAGCATGTCAAC 58.640 55.000 0.00 0.00 41.22 3.18
3303 4937 0.100682 GCTGCTCCTCGTCGTAATCA 59.899 55.000 0.00 0.00 0.00 2.57
3339 4973 3.378427 CCCTGTCAAGTAATAGCTTTGCC 59.622 47.826 0.00 0.00 0.00 4.52
3351 4985 1.131638 TTCTCTGCACCCTGTCAAGT 58.868 50.000 0.00 0.00 0.00 3.16
3408 5042 2.447047 AGGTTCAGGGTGGAAGTTGATT 59.553 45.455 0.00 0.00 0.00 2.57
3439 5073 1.597854 CCTGTTGCGGCTGTTCTGA 60.598 57.895 0.00 0.00 0.00 3.27
3453 5087 0.959372 GCTGCTGTTCTGCATCCTGT 60.959 55.000 4.97 0.00 42.48 4.00
3519 5153 2.035961 GACATTCTCTAGTGGCGCCATA 59.964 50.000 35.23 22.91 0.00 2.74
3643 5295 9.283768 TGAAATGTAAACAACAGATCAGTACAT 57.716 29.630 0.00 0.00 42.70 2.29
3664 5316 3.890756 TGCCACAGAACAGATTGTGAAAT 59.109 39.130 6.21 0.00 45.79 2.17
3804 5456 2.818432 CTGCACCAAAGAGAGAAAGCAT 59.182 45.455 0.00 0.00 0.00 3.79
3839 5491 2.737932 GAAAACCTGGTGCAGCGCAG 62.738 60.000 11.47 1.31 40.08 5.18
3921 5574 7.802738 ACTTTTGAAACAAAACAGGTTAAAGC 58.197 30.769 5.70 0.00 30.22 3.51
3979 5632 0.796312 AGTAAGCAATTCACGGTGCG 59.204 50.000 2.51 0.00 45.62 5.34
4254 5920 0.550914 AGGGTCTGCCAAAGTTGACA 59.449 50.000 0.00 0.00 36.17 3.58
4294 5960 0.110486 ACGCAAGGGACACCAGATTT 59.890 50.000 0.00 0.00 46.39 2.17
4325 5991 0.895530 CACTCTAGGCCGGTTGAAGA 59.104 55.000 1.90 0.31 0.00 2.87
4366 6032 8.095792 TCAGCATGTTTATTTCATTTTGGATGT 58.904 29.630 0.00 0.00 37.40 3.06
4367 6033 8.481974 TCAGCATGTTTATTTCATTTTGGATG 57.518 30.769 0.00 0.00 37.40 3.51
4369 6035 9.585099 GTATCAGCATGTTTATTTCATTTTGGA 57.415 29.630 0.00 0.00 37.40 3.53
4370 6036 9.368674 TGTATCAGCATGTTTATTTCATTTTGG 57.631 29.630 0.00 0.00 37.40 3.28
4410 6081 8.963725 TGAGCAGTTTAGATTTGATCATGATTT 58.036 29.630 10.14 0.00 32.87 2.17
4440 6111 6.188407 AGATGTACTACTGCTCTGGAAGTAA 58.812 40.000 0.00 0.00 33.52 2.24
4451 6125 5.509840 CCTCCACCATTAGATGTACTACTGC 60.510 48.000 0.00 0.00 32.64 4.40
4452 6126 5.509840 GCCTCCACCATTAGATGTACTACTG 60.510 48.000 0.00 0.00 33.41 2.74
4453 6127 4.589374 GCCTCCACCATTAGATGTACTACT 59.411 45.833 0.00 0.00 0.00 2.57
4464 6138 6.998074 CAGTGAATATAAAGCCTCCACCATTA 59.002 38.462 0.00 0.00 0.00 1.90
4471 6145 5.048434 GGCAATCAGTGAATATAAAGCCTCC 60.048 44.000 0.00 0.00 35.63 4.30
4486 6160 2.115052 TGCGGGTTGGCAATCAGT 59.885 55.556 13.32 0.00 40.59 3.41
4501 6175 3.940209 TCCACTTTCAATGGTTGATGC 57.060 42.857 0.00 0.00 39.84 3.91
4506 6180 4.223477 CCCATCATTCCACTTTCAATGGTT 59.777 41.667 0.00 0.00 38.47 3.67
4516 6190 4.320546 TGTTTCATCCCATCATTCCACT 57.679 40.909 0.00 0.00 0.00 4.00


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.